A Biodiversity Content Management System for Research, Education, and Outreach Cynthia Sims Parr University of Maryland, College Park Co-authors Roger Espinosa, Tanya Dewey, George Hammond, Phil Myers, of University of Michigan University of Michigan Museum of Zoology

Biodiversity Biodiversity is the extraordinary variety of all life on Earth - from genes to species to entire ecosystems. -- Smithsonian Institution Monitoring and Assessment of Biodiversity Program

Access

Change

Problems in Biodiversity Databases Diverse users Policy makers Land-use planners Educators, students Laypersons Biologists Complex databases Organism names Habitats Conservation status Reproductive parameters Interactions, etc. Specimen-level and aggregated Changes over time and in different locations Changes in our view of what scale is important Ecological dataset volume rapidly increasing Changes in technology Who will maintain these knowledgebases?

More general scientific data management questions How to design a back-end so that contributors can easily enter data, and end-users can easily retrieve what they want, data managers can make big and small changes How to use the same system for multiple constituent groups research education on different levels outreach to the public

Animal Diversity Web introduction From educational  outreach  science High traffic, 70,000 pages per day Geographically and taxonomically global

Animal Diversity Web challenges Data entry Student contributors Lack domain expertise, technical expertise Few repeat contributors Completeness, Structuring Single template covering all animal phyla would have unnecessary keywords and sections for most taxa Data retrieval To support inquiry education or science, must be able to get data out via queries Users diverse so may not have knowledge of controlled vocabulary What happens when underlying data model changes?

ADW’s “loosely coupled” architecture Weinberger, 2002Nodes separately managed from identifiers used to relate and display them Template Taxonomic names Stylesheets

Taxonomic MySQL database ITIS Howard & Moore birds EMBL reptiles Sources SI mammals CAS fishes WalksCommon names

Creating content Register for workspace Identify subject Receive customized template (increasingly more structured) Text, keywords, data fields Attach references Review, edit, publish

Taxon Filtering for customized templates e.g. template section customized for Aves XML template Taxon filter

Workflow, legacy content Change template elements If new content: receives new template Legacy objects remain semantically tagged for display and search New template elements available for ADW editors

Content display for different audiences

A multi-use database supporting maximum access and minimum barriers to change Content all managed in the same system, with multiple displays (loose coupling, taxon filtering, customized stylesheets) Complex object templates can be created or modified, but legacy data remains semantically marked up and thus available for display and querying New style sheets, updated taxon data Where do we go next?

Vertical integration Example: Biologist studying genetic basis of a behavioral trait that varies across Animalia. ACCTTGAGATAG ACCTTGAGACAG From

+ SEEK ecological ontologies + Animal Behavior ontology (for more information, see me) + Gene Ontology …. Natural history ontology from Animal Diversity Web

Contribution model scales well User involvement fosters engagement Accessible resource for science Scaling, engagement, and interoperability

Acknowledgements ADW team: particularly Phil Myers, Roger Espinosa, Tricia Jones, Tanya Dewey George Hammond BioKIDS team: particularly Nancy Songer Ontologies: Peter Midford and Jennifer Golbeck NSF IERI (UMich) and ITR (UMd) grants Ontologies, manuscript, and presentation can be found at